ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
MSExperiment<Peak1D> ms_peakmap;
std::vector<Int> ms_level(1,2);
(mz_data_file.getOptions()).setMSLevels(ms_level);
mz_data_file.load(in, ms_peakmap);
if (ms_peakmap.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
// FeatureMap<> ms_feat_map;
MzTab mztab_output;
// FeatureXMLFile().load(in, ms_feat_map);
MzTabFile mztab_outfile;
//-------------------------------------------------------------
// get parameters
//-------------------------------------------------------------
Param ams_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to MetaboliteSpectralMatcher", ams_param, 3);
//-------------------------------------------------------------
// do the work
//-------------------------------------------------------------
MetaboliteSpectralMatching ams;
ams.setParameters(ams_param);
ams.run(ms_peakmap, mztab_output);
//std::vector<String> results;
// ams.queryByMass(308.09, results);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
//addDataProcessing_(ms_feat_map, getProcessingInfo_(DataProcessing::IDENTIFICATION_MAPPING));
mztab_outfile.store(out, mztab_output);
//FeatureXMLFile().store(out, ms_feat_map);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**) override
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
String in = getStringOption_("in");
String database = getStringOption_("database");
String spec_db_filename(database);
// default path? retrieve file path in share folder
if (database == "CHEMISTRY/MetaboliteSpectralDB.mzML")
{
// throws Exception::FileNotFound if file does not exist
spec_db_filename = File::find("CHEMISTRY/MetaboliteSpectralDB.mzML");
}
String out = getStringOption_("out");
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_file;
mz_file.setLogType(log_type_);
std::vector<Int> ms_level(1,2);
mz_file.getOptions().setMSLevels(ms_level);
PeakMap ms_peakmap;
mz_file.load(in, ms_peakmap);
if (ms_peakmap.empty())
{
LOG_WARN << "The input file does not contain any spectra.";
return INCOMPATIBLE_INPUT_DATA;
}
MzTab mztab_output;
MzTabFile mztab_outfile;
//-------------------------------------------------------------
// get parameters
//-------------------------------------------------------------
Param ams_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to MetaboliteSpectralMatcher", ams_param, 3);
//-------------------------------------------------------------
// load database
//-------------------------------------------------------------
PeakMap spec_db;
mz_file.load(spec_db_filename, spec_db);
if (spec_db.empty())
{
LOG_WARN << "The spectral library does not contain any spectra.";
return INCOMPATIBLE_INPUT_DATA;
}
//-------------------------------------------------------------
// run spectral library search
//-------------------------------------------------------------
MetaboliteSpectralMatching ams;
ams.setParameters(ams_param);
ams.run(ms_peakmap, spec_db, mztab_output);
//-------------------------------------------------------------
// store results
//-------------------------------------------------------------
mztab_outfile.store(out, mztab_output);
return EXECUTION_OK;
}
